Target (protein/gene name): protein phosphatase type 1, putative (S. mansoni)
*NCBI Gene # or RefSeq#: NC_031496.1
*Protein ID (NP or XP #) or Wolbachia#: XP_018650457.1
*Organism (including strain): schistosoma mansoni
Etiologic Risk Group (see link below):
*/Disease Information (sort of like the Intro to your Mini Research Write up): Schistosoma mansoni is a parasite of humans that is the main agent of the disease schistosomiasis. This disease is spread by contact with fresh water contaminated with the parasites. It is most commonly found among children in underdeveloped countries. Symptoms include abdominal pain, diarrhea, bloody stool, or blood in urine. Long term effects include, liver damage, kidney failure, infertility, or bladder cancer. The parasites lyse red blood cells to gain nutrients essential to their development. They are usually found in the blood vessels of the host. In 2015, almost 252 million people were affected by schistosomiasis. Approximately 4,000 to about 200,000 people die from this disease each year, and most commonly seen throughout Africa and Asia. Schistosomiasis is also listed as one of the most neglected diseases.
Structure (PDB or Homology model) -- PDB # or closest PDB entry if using homology model: -- For Homology Model option: ---- Show pairwise alignment of your BLASTP search in NCBI against the PDB ---- Query Coverage: ---- Max % Identities: ---- % Positives ---- Chain used for homology: Current Inhibitors: (R)-dehydrolipoic acid
Expression Information (has it been expressed in bacterial cells): n/a
Purification Method: n/a
Image of protein (PyMol with features delineated and shown separately): no structure in the PDB
*Amino Acid Sequence (paste as text only - not as screenshot or as 'code'):
Molecular Weight of your protein in kiloDaltons using the Expasy ProtParam website: 17501.94 kD
Molar Extinction coefficient of your protein at 280 nm wavelength: Ext. coefficient 12865 Abs 0.1% (=1 g/l) 0.735, assuming all pairs of Cys residues form cystines
Ext. coefficient 12490 Abs 0.1% (=1 g/l) 0.714, assuming all Cys residues are reduced
TMpred graph Image (http://www.ch.embnet.org/software/TMPRED_form.html). Input your amino acid sequence to it. *CDS Gene Sequence (paste as text only): atggcgaccgaactgcgcaccaacgtgaaagcggaacgcgaagaacagccggcgaccgtg gcggatgtgaaccagccgctgctgattcgcggcaccagccatgcgcagaccgtggataac gaaaacaccctgccgagcagcagccatggcccggcgattcattgggcggaaggcaccatt gataacgaatttatgggcaaaaaaaaaagcagctgctgctgcatttatgaaaaaccgcgc aaatggaacgaaagcagcagcagcagcagcgatgatagcgatccgagcccggatgataac gatgataccaacaaacagaacaccaacaaacatacccattgcaccgaaaactgccgcggc cataccaaacgctgctttcgcaaaaaaaaaaacaacaaagatagcaacagcgaaaacttt gaaaaaccgaccccgagcagcagcgattttaacccgaacggcctgtgcagc
*GC% Content for gene: 52.866242%
*CDS Gene Sequence (codon optimized) - copy from output of Primer Design Protocol (paste as text only): ATG GCA ACA GAA TTA CGA ACT AAT GTT AAA GCT GAG AGA GAG GAA CAG CCA GCT ACT GTC GCA GAC GTG AAT CAA CCT TTG CTT ATA CGT GGC ACA TCA CAT GCCCAA ACA GTG GAT AAT GAG AAT ACA CTT CCA TCT TCA AGT CAT GGC CCT GCC ATC CAC TGG GCC GAG GGT ACT ATA GAT AAC GAG TTC ATG GGC AAG AAG AAG AGTTCT TGC TGT TGT ATC TAC GAA AAA CCT CGA AAA TGG AAC GAA TCT AGT TCT TCA AGT TCA GAT GAC TCT GAC CCA TCT CCT GAC GAC AAT GAC GAC ACA AAT AAACAA AAC ACT AAT AAA CAT ACA CAT TGC ACT GAA AAC TGT AGA GGA CAT ACT AAG AGA TGC TTC CGA AAG AAG AAG AAT AAC AAG GAC TCA AAC TCT GAA AAC TTTGAA AAG CCT ACT CCT AGT AGT AGT GAC TTC AAC CCA AAT GGA TTA TGT AGC
*GC% Content for gene (codon optimized): 41.613588%
Do Not Need this info for Spring (but still copy these lines to your Target page for now) Primer design results for pNIC-Bsa4 cloning (list seqeunces of all of your ~40 nt long primers): (link to DNA Works output text file - that should be saved in your Google Docs folder after you did the primer design protocol) -- Ask a mentor, Dr. B, or a fellow researcher -how to link a GDocs file if you are not sure how to.
Primer design results for 'tail' primers (this is just 2 sequences): **
*NCBI Gene # or RefSeq#: NC_031496.1
*Protein ID (NP or XP #) or Wolbachia#: XP_018650457.1
*Organism (including strain): schistosoma mansoni
Etiologic Risk Group (see link below):
*/Disease Information (sort of like the Intro to your Mini Research Write up):
Schistosoma mansoni is a parasite of humans that is the main agent of the disease schistosomiasis. This disease is spread by contact with fresh water contaminated with the parasites. It is most commonly found among children in underdeveloped countries. Symptoms include abdominal pain, diarrhea, bloody stool, or blood in urine. Long term effects include, liver damage, kidney failure, infertility, or bladder cancer. The parasites lyse red blood cells to gain nutrients essential to their development. They are usually found in the blood vessels of the host. In 2015, almost 252 million people were affected by schistosomiasis. Approximately 4,000 to about 200,000 people die from this disease each year, and most commonly seen throughout Africa and Asia. Schistosomiasis is also listed as one of the most neglected diseases.
Link to TDR Targets page (if present):
http://tdrtargets.org/targets/view?gene_id=282815
Link to Gene Database page (NCBI, EuPath databases -e.g. TryTryp, PlasmoDB, etc - or PATRIC, etc.)
Essentiality of this protein:
https://www.ncbi.nlm.nih.gov/gene/8348767
Is it a monomer or multimer as biological unit? (make prediction at http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html): Ortholog of A. thaliana: monomer
Complex of proteins?: No
Druggable Target (list number or cite evidence from a paper/database showing druggable in another organism):
https://www.ebi.ac.uk/chembldb/index.php/target/inspect/10083
*EC#: 3.1.3.17
Link to BRENDA EC# page: http://www.brenda-enzymes.org/enzyme.php?ecno=3.1.3.17
Enzyme Assay information (spectrophotometric, coupled assay ?, reagents):
-- link to Sigma (or other company) page for assay (see Sigma links below)
-- -or link (or citation) to paper that contains assay information
-- links to assay reagents (substrates) pages.
--- List cost and quantity of substrate reagents, supplier, and catalog #
spectrophotometric using pNPP enzyme assay
http://www.uvm.edu/~bio1and2/lab/Lab%20manuals%20Fall%202011/Enzyme%20Activity%20Phosphatase.pdf
https://www.thermofisher.com/order/catalog/product/34045
Structure (PDB or Homology model)
-- PDB # or closest PDB entry if using homology model:
-- For Homology Model option:
---- Show pairwise alignment of your BLASTP search in NCBI against the PDB
---- Query Coverage:
---- Max % Identities:
---- % Positives
---- Chain used for homology:
Current Inhibitors: (R)-dehydrolipoic acid
Expression Information (has it been expressed in bacterial cells): n/a
Purification Method: n/a
Image of protein (PyMol with features delineated and shown separately): no structure in the PDB
*Amino Acid Sequence (paste as text only - not as screenshot or as 'code'):
<span style="color: #222222; font-family: monospace,monospace; font-size: 14.04px;"> 10 20 30 40 50 MATELRTNVK AEREEQPATV ADVNQPLLIR GTSHAQTVDN ENTLPSSSHG 60 70 80 90 100 PAIHWAEGTI DNEFMGKKKS SCCCIYEKPR KWNESSSSSS DDSDPSPDDN 110 120 130 140 150 DDTNKQNTNK HTHCTENCRG HTKRCFRKKK NNKDSNSENF EKPTPSSSDF NPNGLCS</span>*length of your protein in Amino AcidsMolecular Weight of your protein in kiloDaltons using the Expasy ProtParam website: 17501.94 kD
Molar Extinction coefficient of your protein at 280 nm wavelength:
Ext. coefficient 12865
Abs 0.1% (=1 g/l) 0.735, assuming all pairs of Cys residues form cystines
Ext. coefficient 12490
Abs 0.1% (=1 g/l) 0.714, assuming all Cys residues are reduced
TMpred graph Image (http://www.ch.embnet.org/software/TMPRED_form.html). Input your amino acid sequence to it.
*CDS Gene Sequence (paste as text only):
atggcgaccgaactgcgcaccaacgtgaaagcggaacgcgaagaacagccggcgaccgtg gcggatgtgaaccagccgctgctgattcgcggcaccagccatgcgcagaccgtggataac gaaaacaccctgccgagcagcagccatggcccggcgattcattgggcggaaggcaccatt gataacgaatttatgggcaaaaaaaaaagcagctgctgctgcatttatgaaaaaccgcgc aaatggaacgaaagcagcagcagcagcagcgatgatagcgatccgagcccggatgataac gatgataccaacaaacagaacaccaacaaacatacccattgcaccgaaaactgccgcggc cataccaaacgctgctttcgcaaaaaaaaaaacaacaaagatagcaacagcgaaaacttt gaaaaaccgaccccgagcagcagcgattttaacccgaacggcctgtgcagc
*GC% Content for gene: 52.866242%
*CDS Gene Sequence (codon optimized) - copy from output of Primer Design Protocol (paste as text only):
ATG GCA ACA GAA TTA CGA ACT AAT GTT AAA GCT GAG AGA GAG GAA CAG CCA GCT ACT GTC GCA GAC GTG AAT CAA CCT TTG CTT ATA CGT GGC ACA TCA CAT GCCCAA ACA GTG GAT AAT GAG AAT ACA CTT CCA TCT TCA AGT CAT GGC CCT GCC ATC CAC TGG GCC GAG GGT ACT ATA GAT AAC GAG TTC ATG GGC AAG AAG AAG AGTTCT TGC TGT TGT ATC TAC GAA AAA CCT CGA AAA TGG AAC GAA TCT AGT TCT TCA AGT TCA GAT GAC TCT GAC CCA TCT CCT GAC GAC AAT GAC GAC ACA AAT AAACAA AAC ACT AAT AAA CAT ACA CAT TGC ACT GAA AAC TGT AGA GGA CAT ACT AAG AGA TGC TTC CGA AAG AAG AAG AAT AAC AAG GAC TCA AAC TCT GAA AAC TTTGAA AAG CCT ACT CCT AGT AGT AGT GAC TTC AAC CCA AAT GGA TTA TGT AGC
*GC% Content for gene (codon optimized): 41.613588%
Do Not Need this info for Spring (but still copy these lines to your Target page for now)
Primer design results for pNIC-Bsa4 cloning (list seqeunces of all of your ~40 nt long primers):
(link to DNA Works output text file - that should be saved in your Google Docs folder after you did the primer design protocol)
-- Ask a mentor, Dr. B, or a fellow researcher -how to link a GDocs file if you are not sure how to.
Primer design results for 'tail' primers (this is just 2 sequences):
**